def test_decompose_alobestia(self):
super_cluster = Cluster(read=PK, write= BED, tag_length=130)
super_cluster.read_line("chrX 2895999 2896606 10:1|42:2|14:6|33:7|31:10|6:9|4:10|25:9|2:10|1:12|3:13|5:14|6:15|5:12|4:13|5:14|4:13|8:15|13:16|6:18|2:19|5:16|15:17|17:18|29:17|2:16|1:14|2:13|1:16|5:15|6:14|5:13|4:12|5:11|4:12|8:10|10:9|3:11|6:9|7:8|8:7|7:10|2:9|37:10|12:12|26:9|2:8|2:10|18:12|24:12|9:9|37:8|40:6|2:4|18:2")
tags = super_cluster.decompose()
for tag in tags:
self.assertEqual(len(tag), 130)
class TestCoreObjects(unittest.TestCase):
def setUp(self):
self.tag_list_short = [Cluster('chr1', 1, 10, read=PK), Cluster('chr1', 5, 14, read=PK)]
self.cluster_short = Cluster(rounding=True, read=PK)
self.cluster_short.read_line('chr1 1 14 4:1|6:2|4:1')
self.pk_cluster = Cluster(rounding=True, read=PK, write=PK)
self.pk_cluster.read_line('chr1 1 15 4:1|1:2|2:1|3:4|2:5|2:2|1:1')
self.bed_tag = Cluster(read=BED, write=BED, rounding=True)
self.bed_tag.read_line('chr1 1 100 hola 666 +')
self.cluster1 = Cluster(rounding=True, read=PK)
self.cluster2 = Cluster(rounding=True, read=PK)
def test_cached_cluster(self):
cached = Cluster(read=BED, cached=True, rounding=True)
for i in xrange(0, 200):
cached.read_line('chr1 %s %s hola 666 +'%(i, i+99))
self.assertEqual(cached.write_line(), 'chr1\t0\t298\t1:1|1:2|1:3|1:4|1:5|1:6|1:7|1:8|1:9|1:10|1:11|1:12|1:13|1:14|1:15|1:16|1:17|1:18|1:19|1:20|1:21|1:22|1:23|1:24|1:25|1:26|1:27|1:28|1:29|1:30|1:31|1:32|1:33|1:34|1:35|1:36|1:37|1:38|1:39|1:40|1:41|1:42|1:43|1:44|1:45|1:46|1:47|1:48|1:49|1:50|1:51|1:52|1:53|1:54|1:55|1:56|1:57|1:58|1:59|1:60|1:61|1:62|1:63|1:64|1:65|1:66|1:67|1:68|1:69|1:70|1:71|1:72|1:73|1:74|1:75|1:76|1:77|1:78|1:79|1:80|1:81|1:82|1:83|1:84|1:85|1:86|1:87|1:88|1:89|1:90|1:91|1:92|1:93|1:94|1:95|1:96|1:97|1:98|1:99|101:100|1:99|1:98|1:97|1:96|1:95|1:94|1:93|1:92|1:91|1:90|1:89|1:88|1:87|1:86|1:85|1:84|1:83|1:82|1:81|1:80|1:79|1:78|1:77|1:76|1:75|1:74|1:73|1:72|1:71|1:70|1:69|1:68|1:67|1:66|1:65|1:64|1:63|1:62|1:61|1:60|1:59|1:58|1:57|1:56|1:55|1:54|1:53|1:52|1:51|1:50|1:49|1:48|1:47|1:46|1:45|1:44|1:43|1:42|1:41|1:40|1:39|1:38|1:37|1:36|1:35|1:34|1:33|1:32|1:31|1:30|1:29|1:28|1:27|1:26|1:25|1:24|1:23|1:22|1:21|1:20|1:19|1:18|1:17|1:16|1:15|1:14|1:13|1:12|1:11|1:10|1:9|1:8|1:7|1:6|1:5|1:4|1:3|1:2|1:1\t100.0\t+\t149\t20000.0\n')
##################### REGION TESTS ############################
def test_FDR(self):
r = Region('', 1, 1999)
tags = []
for i in range(0, 50):
c = Cluster()
c.read_line('chr4 %s %s 20:1'%(i, i+50))
tags.append(c)
r.add_tags(tags, True)
c = Cluster()
c.read_line('chr4 55555 55558 7:1')
r.add_tags(c)
result = r.get_FDR_clusters()
self.assertEqual(len(result), 1)
def test_get_profile(self):
r = Region(start=1, end=1999)
c = Cluster(read=BED)
c.read_line('chr4 1 40')
r.add_tags(c, True)
c = Cluster(read=BED, read_half_open=True)
c.read_line('chr4 400 500')
r.add_tags(c, True)
meta = r.get_metacluster()
self.assertEqual(meta._levels, [[40, 1.0], [360, 0.0], [100, 1.0]])
def test_region_swap_rpkm(self):
total_reads = 400000000
total_reads_b = 500000000
r = Region("chr1", 1, 1000, name2="bla")
c = Cluster(read=BED)
c.read_line('chr1 1 40')
r.add_tags(c)
c = Cluster(read=BED)
c.read_line('chr1 2 40')
r.add_tags(c)
c = Cluster(read=BED)
c.read_line('chr1 3 40')
r.add_tags(c)
r2 = Region("chr1", 1, 1000, name2="bla")
c = Cluster(read=BED)
c.read_line('chr1 100 140')
r2.add_tags(c)
c = Cluster(read=BED)
c.read_line('chr1 101 140')
r2.add_tags(c)
c = Cluster(read=BED)
c.read_line('chr1 102 140')
r2.add_tags(c)
swap1, swap2 = r.swap(r2)
len(r.tags), len(r2.tags), len(swap1.tags), len(swap2.tags), r.rpkm(total_reads), r2.rpkm(total_reads_b), swap1.rpkm((total_reads+total_reads_b)/2), swap2.rpkm((total_reads+total_reads_b)/2) #TODO dont know how to test this
##################### CONVERSION TESTS ############################################
def test_simple_ucsc_representation(self):
"""Confirmed visually at the UCSC browser
track name=simple_read visibility=full
chr3 101 200 noname 555 +
track type=wiggle_0 name=the_test visibility=full
chr3 101 200 1
"""
cluster = Cluster(read=BED, write=WIG, read_half_open=True, write_half_open=True, rounding = True, cached=True)
cluster.read_line('chr3 101 200 noname 555 +')
self.assertEqual(cluster.write_line(), 'chr3\t101\t200\t1\n')
def test_bed_to_half_open_wig(self):
"""Confirmed visually at the UCSC browser
track name=simple_cluster visibility=full
chr1 1 100 hola 666 +
chr1 10 130 hola 666 +
track type=wiggle_0 name=the_test visibility=full
chr1 1 10 1
chr1 10 100 2
chr1 100 130 1
"""
cluster = Cluster(read=BED, write=WIG, read_half_open=True, write_half_open=True, rounding = True, cached=True)
cluster.read_line('chr1 1 100 hola 666 +')
cluster.read_line('chr1 10 130 hola 666 +')
self.assertEqual(cluster.write_line(), 'chr1\t1\t10\t1\nchr1\t10\t100\t2\nchr1\t100\t130\t1\n')
def read_and_extend(self, cluster, line, extension):
cluster_aux = Cluster(read=BED, write=BED, read_half_open=True, write_half_open=True, rounding = True)
if cluster.is_empty():
cluster.read_line(line)
cluster.extend(extension)
#print cluster.write_line(), cluster._profile
else:
cluster_aux.read_line(line)
cluster_aux.extend(extension)
#print cluster_aux.write_line(), cluster_aux._profile
cluster += cluster_aux
#print cluster.write_line()
return cluster
def test_pk_printing(self):
#PENDING
cluster = Cluster()
cluster.read_line('chr1 1 100 10:0.76|10:0.001|80:2')
#print cluster.absolute_split(threshold=0)
#print cluster.write_line()
def test_split_subtract_result(self):
sub_result = Cluster(write_half_open=True, cached=True)
sub_result.read_line('chr4 1 300 20:1|40:0|20:3|20:0.3|10:-6|80:1|10:0')
clusters = sub_result.absolute_split(threshold=0)
result = []
result.append('chr4\t0\t20\t20:1.00\t1.0\t.\t10\t20.0\n')
result.append('chr4\t60\t100\t20:3.00|20:0.30\t3.0\t.\t70\t66.0\n')
result.append('chr4\t110\t190\t80:1.00\t1.0\t.\t150\t80.0\n')
for i in range(0, len(clusters)):
self.assertEqual(clusters[i].write_line(), result[i])
def test_bed_to_wig_extended(self):
"""Confirmed visually at the UCSC browser
track name=unextended_cluster visibility=full
chr1 1 36 hola 666 +
chr1 2 37 hola 666 +
chr1 71 106 hola 666 -
chr1 73 108 hola 666 -
track name=extended_cluster visibility=full
chr1 1 101 hola 666 +
chr1 2 102 hola 666 +
chr1 6 106 hola 666 -
chr1 8 108 hola 666 -
track type=wiggle_0 name=extended_wig visibility=full
chr1 1 2 1
chr1 2 6 2
chr1 6 8 3
chr1 8 101 4
chr1 101 102 3
chr1 102 106 2
chr1 106 108 1
"""
cluster = Cluster(read=BED, write=WIG, read_half_open=True, write_half_open=True, rounding = True)
cluster = self.read_and_extend(cluster, 'chr1 1 36 hola 666 +', 100)
cluster = self.read_and_extend(cluster, 'chr1 2 37 hola 666 +', 100)
cluster = self.read_and_extend(cluster, 'chr1 71 106 hola 666 -', 100)
cluster = self.read_and_extend(cluster, 'chr1 73 108 hola 666 -', 100)
result = Cluster(read=WIG, write=WIG, read_half_open=True, write_half_open=True, rounding = True)
result.read_line('chr1 1 2 1')
result.read_line('chr1 2 6 2')
result.read_line('chr1 6 8 3')
result.read_line('chr1 8 101 4')
result.read_line('chr1 101 102 3')
result.read_line('chr1 102 106 2')
result.read_line('chr1 106 108 1')
self.assertEqual(cluster.write_line(), result.write_line())
def test_sub_fast(self):
#random/experiment.pk
experiment = Cluster(rounding=True)
experiment.read_line("chr1 1 1107 101:2|7:1 2.0 . 263 238.0")
control = Cluster()
control.read_line( "chr1 46 1222 47:1|54:2|47:1 2.0 . 71331 202.0")
experiment -= control
self.assertEqual(experiment.write_line(), 'chr1\t1\t92\t45:2|47:1\t2.0\t.\t23\t137.0\n')#chr1 1 92 45:2|47:1 2.0 . 23 137.0
"""
def test_sub_fast(self): BACUP
#random/experiment.pk
experiment = Cluster(rounding=True)
experiment.read_line("chr17 60 320 59:1.00|42:2.00|52:1.00|101:2.00|7:1.00 2.0 . 71201 404.0")
print experiment.write_line()
control = Cluster()
#random/control.pk
control.read_line("chr17 83 183 101:1.00 1.0 . 71133 101.0")
experiment -= control
print experiment._levels
print experiment.write_line()
control2 = Cluster()
control2.read_line("chr17 258 405 47:1.00|54:2.00|47:1.00 2.0 . 71331 202.0")
experiment -= control2
print experiment._levels
print experiment.write_line()
#Correcto
#chr17 184 304 29:1.00|45:2.00|47:1.00 2.0 . 71235 166.0"""
def test_strand_add(self):
c = Cluster(read=BED, cached=True)
c2 = Cluster(read=BED, cached=True)
c3 = Cluster(read=BED, cached=True)
c4 = Cluster(read=BED, cached=True)
c.read_line("chr1 1 100 0 0 +")
c2.read_line("chr1 1 100 0 0 +")
c3.read_line("chr1 1 100 0 0 -")
c4.read_line("chr1 1 100 0 0 -")
plus = c + c2
minus = c3 + c4
dot = c2 + c3
self.assertEqual(plus.strand, PLUS_STRAND)
self.assertEqual(dot.strand, NO_STRAND)
self.assertEqual(minus.strand, MINUS_STRAND)
def test_internal_representations(self):
"Este test prueba la integridad interna de los datos. Si no pasa, MAL"
bed = Cluster(read=BED, cached=True, read_half_open=True)
bed.read_line('chr1 0 100 2345 hola +')
bed._flush_tag_cache()
pk = Cluster(read=PK)
pk.read_line('chr1 1 100 100:1')
open_wig = Cluster(read=WIG, read_half_open=True)
open_wig.read_line('chr1 0 100 1')
wig= Cluster(read=WIG)
wig.read_line('chr1 1 100 1')
self.assertEqual(bed._levels, pk._levels)
self.assertEqual(wig._levels, pk._levels)
self.assertEqual(wig._levels, bed._levels)
self.assertEqual(wig._levels, open_wig._levels)
self.assertEqual(wig.start, open_wig.start)
self.assertEqual(wig.end, open_wig.end)
self.assertEqual(wig._levels[0], [100, 1.0])
def test_pk_to_half_open_wig(self):
cluster = Cluster(read=PK, write=WIG, write_half_open=True, rounding=True)
cluster.read_line('chr1 1 15 4:1|1:2|2:1|3:4|2:5|2:2|1:1')
self.assertEqual(cluster.write_line(),'chr1\t0\t4\t1\nchr1\t4\t5\t2\nchr1\t5\t7\t1\nchr1\t7\t10\t4\nchr1\t10\t12\t5\nchr1\t12\t14\t2\nchr1\t14\t15\t1\n')
def test_wig_read_write(self):
cluster = Cluster(read=WIG, write=WIG, read_half_open=True, write_half_open=True, rounding=True)
cluster.read_line('chr2 1 10 1')
cluster.read_line('chr2 10 16 2')
cluster.read_line('chr2 16 26 1')
self.assertEqual(cluster.write_line(), 'chr2\t1\t10\t1\nchr2\t10\t16\t2\nchr2\t16\t26\t1\n')
cluster.write_as(WIG, False)
self.assertEqual(cluster.write_line(), 'chr2\t2\t10\t1\nchr2\t11\t16\t2\nchr2\t17\t26\t1\n')
def test_pk_to_variable_wig(self):
cluster = Cluster(read=PK, write=VARIABLE_WIG)
cluster.read_line('chr1 1599889 1600275 61:1.77|52:2.65|7:1.77|4:2.65|6:3.54|9:2.65|19:3.54|6:4.42|14:5.31|1:6.19|11:7.08|1:7.96|20:7.08|9:7.96|1:8.85|13:9.73|1:10.62|8:11.50|5:12.39|6:13.27|2:12.39|1:13.27|1:14.16|11:15.04|19:14.16|6:13.27|14:12.39|1:11.50|11:10.62|21:9.73|9:8.85|1:7.96|13:7.08|1:6.19|8:5.31|5:4.42|2:3.54|6:2.65|1:1.77')
self.assertEqual(cluster.write_line(), '1599889\t1.77\n1599909\t1.77\n1599929\t1.77\n1599949\t2.606\n1599969\t2.65\n1599989\t2.342\n1600009\t2.9615\n1600029\t3.628\n1600049\t5.2645\n1600069\t7.124\n1600089\t7.476\n1600109\t10.173\n1600129\t12.918\n1600149\t14.556\n1600169\t13.362\n1600189\t11.372\n1600209\t9.73\n1600229\t8.053\n1600249\t5.3085\n')
def test_bed_reader(self):
self.assertEqual(self.bed_tag.start, 1)
self.assertEqual(self.bed_tag.end, 100)
self.assertEqual(self.bed_tag.name2, 'hola')
self.assertEqual(self.bed_tag.strand, '+')
def test_bed_writer(self):
self.assertEqual(self.bed_tag.write_line(), 'chr1\t1\t100\thola\t666\t+\n')
def test_pk_reader_writer(self):
self.assertEqual(self.pk_cluster.write_line(), 'chr1\t1\t15\t4:1|1:2|2:1|3:4|2:5|2:2|1:1\t5.0\t.\t11\t35.0\n')
def test_pk_to_bed(self):
self.cluster_short.set_tag_length(10)
self.cluster_short.write_as(BED)
self.assertEqual(self.cluster_short.write_line(), 'chr1\t1\t10\tnoname\t0\t.\nchr1\t5\t14\tnoname\t0\t.\n')
def test_bed_half_open_to_wig_half_open(self):
cluster = Cluster(read=BED, write=WIG, read_half_open=True, write_half_open=True, rounding=True)
cluster.read_line('chr1\t0\t100\t666\thola\t+\n')
cluster.read_line('chr1\t1\t101\t666\thola\t+\n')
self.assertEqual(cluster.write_line(), 'chr1\t0\t1\t1\nchr1\t1\t100\t2\nchr1\t100\t101\t1\n')
def test_bed_half_open_to_wig_half_open2(self):
cluster = Cluster(read=BED, write=WIG, read_half_open=True, write_half_open=True, rounding=True, cached=True)
cluster2 = Cluster(read=BED, write=WIG, read_half_open=True, write_half_open=True, rounding=True, cached=True)
cluster3 = Cluster(read=BED, write=WIG, read_half_open=True, write_half_open=True, rounding=True, cached=True)
result = Cluster(read=BED, write=WIG, read_half_open=True, write_half_open=True, rounding=True)
extension = 130
result.read_line('chr1 156 192 id:7043691 1000 +')
result.extend(extension)
cluster.read_line('chr1 241 277 id:916714 1000 +')
cluster.extend(extension)
result +=cluster
cluster2.read_line('chr1 241 277 id:916714 1000 +')
cluster2.extend(extension)
result +=cluster2
cluster3.read_line('chr1 241 277 id:6880101 1000 +')
cluster3.extend(extension)
result +=cluster3
self.assertEqual(result.write_line(), 'chr1\t156\t241\t1\nchr1\t241\t286\t4\nchr1\t286\t371\t3\n')
def test_openwig_to_pk(self):
cluster = Cluster(read=WIG, write=PK, read_half_open=True, rounding = True)
cluster.read_line('chr1 1599888 1599949 1.77')
cluster.read_line('chr1 1599949 1600001 2.65')
cluster.read_line('chr1 1600001 1600008 1.77')
cluster.read_line('chr1 1600008 1600012 2.65')
cluster.read_line('chr1 1600012 1600018 3.54')
cluster.read_line('chr1 1600018 1600027 2.65')
cluster.read_line('chr1 1600027 1600046 3.54')
cluster.read_line('chr1 1600046 1600052 4.42')
cluster.read_line('chr1 1600052 1600066 5.31')
cluster.read_line('chr1 1600066 1600067 6.19')
cluster.read_line('chr1 1600067 1600078 7.08')
cluster.read_line('chr1 1600078 1600079 7.96')
cluster.read_line('chr1 1600079 1600099 7.08')
cluster.read_line('chr1 1600099 1600108 7.96')
cluster.read_line('chr1 1600108 1600109 8.85')
cluster.read_line('chr1 1600109 1600122 9.73')
cluster.read_line('chr1 1600122 1600123 10.62')
cluster.read_line('chr1 1600123 1600131 11.50')
cluster.read_line('chr1 1600131 1600136 12.39')
cluster.read_line('chr1 1600136 1600138 13.27')
cluster.read_line('chr1 1600138 1600142 13.27')
cluster.read_line('chr1 1600142 1600144 12.39')
cluster.read_line('chr1 1600144 1600145 13.27')
cluster.read_line('chr1 1600145 1600146 14.16')
cluster.read_line('chr1 1600146 1600157 15.04')
cluster.read_line('chr1 1600157 1600176 14.16')
cluster.read_line('chr1 1600176 1600182 13.27')
cluster.read_line('chr1 1600182 1600196 12.39')
cluster.read_line('chr1 1600196 1600197 11.50')
cluster.read_line('chr1 1600197 1600208 10.62')
cluster.read_line('chr1 1600208 1600229 9.73')
cluster.read_line('chr1 1600229 1600238 8.85')
cluster.read_line('chr1 1600238 1600239 7.96')
cluster.read_line('chr1 1600239 1600252 7.08')
cluster.read_line('chr1 1600252 1600253 6.19')
cluster.read_line('chr1 1600253 1600261 5.31')
cluster.read_line('chr1 1600261 1600266 4.42')
cluster.read_line('chr1 1600266 1600268 3.54')
cluster.read_line('chr1 1600268 1600274 2.65')
cluster.read_line('chr1 1600274 1600275 1.77')
cluster2 = Cluster(read=PK, write=WIG, write_half_open=True)
cluster2.read_line('chr1 1599889 1600275 61:1.77|52:2.65|7:1.77|4:2.65|6:3.54|9:2.65|19:3.54|6:4.42|14:5.31|1:6.19|11:7.08|1:7.96|20:7.08|9:7.96|1:8.85|13:9.73|1:10.62|8:11.50|5:12.39|2:13.27|4:13.27|2:12.39|1:13.27|1:14.16|11:15.04|19:14.16|6:13.27|14:12.39|1:11.50|11:10.62|21:9.73|9:8.85|1:7.96|13:7.08|1:6.19|8:5.31|5:4.42|2:3.54|6:2.65|1:1.77')
self.assertEqual(cluster, cluster2)
def test_bed_to_wig_using_clusters(self):
cluster = Cluster(read=BED, write=WIG, rounding = True, cached=True)
cluster.read_line('chr1 1 100 hola 666 +')
cluster.read_line('chr1 10 130 hola 666 +')
self.assertEqual(cluster.write_line(), 'chr1\t1\t9\t1\nchr1\t10\t100\t2\nchr1\t101\t130\t1\n')
def test_overlap(self):
cluster1 = Cluster(read=BED)
cluster1.read_line('chr1 1 100 hola 666 +')
cluster2 = Cluster(read=BED)
cluster2.read_line('chr1 51 200 hola 666 +')
cluster3 = Cluster(read=PK)
cluster3.read_line('chr3 1 100 100:1')
cluster4 = Cluster(read=BED)
cluster4.read_line('chr5 1 1000 hola 666 +')
cluster5 = Cluster(read=PK)
cluster5.read_line('chr5 1 300 300:1')
cluster6 = Cluster(read=BED)
cluster6.read_line('chr5 100 900 hola 666 +')
cluster_discard = Cluster(read=BED, read_half_open=True)
cluster_discard.read_line('chrX 61836251 61836287 id:105282 1000 +')
cluster_satellite = Cluster(read=BED)
cluster_satellite.read_line('chrX 61836270 61837703 Satellite')
self.assertEqual(cluster_discard.overlap(cluster_satellite), 0.5)
self.assertEqual(cluster1.overlap(cluster3), 0)
self.assertEqual(cluster1.overlap(cluster1), 1)
self.assertEqual(cluster1.overlap(cluster2), 0.5)
#print cluster4.overlap(cluster5)
#print cluster5.overlap(cluster4)
#print cluster4.overlap(cluster6)
def test_subtraction_and_split(self):
r5_cluster = Cluster(read=BED, read_half_open=True)
t0_cluster1 = Cluster(read=BED, read_half_open=True)
t0_cluster2 = Cluster(read=BED, read_half_open=True)
t0_cluster3 = Cluster(read=BED, read_half_open=True)
r5_cluster.normalize_factor = 0.839874264736
r5_cluster.read_line('chr1 74953355 74953485 id:3920202 1000 +')
r5_cluster.read_line('chr1 74953361 74953491 id:10182740 1000 +')
r5_cluster.read_line('chr1 74953455 74953585 id:9188423 1000 +')
r5_cluster.read_line('chr1 74953455 74953585 id:9188423 1000 +')
r5_cluster.read_line('chr1 74953558 74953688 id:386762 1000 -')
r5_cluster.read_line('chr1 74953558 74953688 id:6854318 1000 -')
r5_cluster.read_line('chr1 74953600 74953730 id:2599120 1000 -')
r5_cluster.read_line('chr1 74953619 74953749 id:5380695 1000 -')
t0_cluster1.read_line('chr1 74953283 74953413 id:8980785 1000 +')
t0_cluster2.read_line('chr1 74953440 74953570 id:9844290 1000 -')
t0_cluster3.read_line('chr1 74953785 74953915 id:1331588 1000 +')
"""
TO no extendido
chr1 283 319 id:8980785 1000 +
chr1 534 570 id:9844290 1000 -
chr1 785 821 id:1331588 1000 +
"""
r5_cluster -= t0_cluster1
r5_cluster -= t0_cluster2
r5_cluster -= t0_cluster3
#print 'AQUI:', r5_cluster.write_line()
"""r5_cluster.read_line('chr1 74953302 74953432 id:8971336 1000 -')
r5_cluster.read_line('chr1 74953340 74953470 id:7068001 1000 -')
r5_cluster.read_line('chr1 74953345 74953475 id:5184564 1000 -')
r5_cluster.read_line('chr1 74953355 74953485 id:3920202 1000 +')"""
"""r5_cluster.read_line('chr1 74953648 74953778 id:994315 1000 +')
r5_cluster.read_line('chr1 74953655 74953785 id:227378 1000 +')
r5_cluster.read_line('chr1 74953655 74953785 id:227378 1000 +')
r5_cluster.read_line('chr1 74953655 74953785 id:227378 1000 +')
r5_cluster.read_line('chr1 74953655 74953785 id:227378 1000 +')
r5_cluster.read_line('chr1 74953659 74953789 id:7728529 1000 +')
r5_cluster.read_line('chr1 74953659 74953789 id:7728529 1000 +')
r5_cluster.read_line('chr1 74953663 74953793 id:4431027 1000 +')
r5_cluster.read_line('chr1 74953663 74953793 id:4431027 1000 +')
r5_cluster.read_line('chr1 74953663 74953793 id:8828390 1000 +')
r5_cluster.read_line('chr1 74953668 74953798 id:10143275 1000 +')
r5_cluster.read_line('chr1 74953668 74953798 id:10143275 1000 +')
r5_cluster.read_line('chr1 74953673 74953803 id:2638800 1000 +')
r5_cluster.read_line('chr1 74953673 74953803 id:9469850 1000 +')
r5_cluster.read_line('chr1 74953686 74953816 id:9965178 1000 -')
r5_cluster.read_line('chr1 74953692 74953822 id:6509113 1000 +')
r5_cluster.read_line('chr1 74953692 74953822 id:7927956 1000 +')
r5_cluster.read_line('chr1 74953720 74953850 id:3496791 1000 -')
r5_cluster.read_line('chr1 74953720 74953850 id:3496791 1000 -')
r5_cluster.read_line('chr1 74953720 74953850 id:3496791 1000 -')
r5_cluster.read_line('chr1 74953720 74953850 id:3496791 1000 -')"""
def test_trim(self):
cluster = Cluster(rounding=True)
cluster.read_line('chr21 1 10 1:1|1:2|3:5|1:1|1:4|1:3|2:1')
cluster.trim(absolute=3)
self.assertEqual(cluster.write_line(), 'chr21\t3\t8\t3:5|1:1|1:4|1:3\t5.0\t.\t4\t23.0\n')
def test_eland_read_write(self):
cluster = Cluster(read=ELAND, write=ELAND)
cluster.read_line('>EAS38_1_1_113_546 TAGAATAGGCGAGAATAAAGATGTTGTCTTAGAAT U0 1 0 0 chr2.fa 199668361 R ..')
self.assertEqual(cluster.write_line(), '>EAS38_1_1_113_546\tTAGAATAGGCGAGAATAAAGATGTTGTCTTAGAAT\tU0\t1\t0\t0\tchr2.fa\t199668361\tR\t..\t26A\n')
def test_eland(self):
cluster = Cluster(read=ELAND)
cluster.read_line('>EAS38_1_1_113_546 TAGAATAGGCGAGAATAAAGATGTTGTCTTAGAAT U0 1 0 0 chr2.fa 199668361 R ..')
cluster.read_line('>EAS38_1_1_113_546 TAGAATAGGCGAGAATAAAGATGTTGTCTTAGAAT U0 1 0 0 chr2.fa 199668362 R ..')
self.assertEqual(cluster.write_line(), 'chr2\t199668361\t199668396\t1:1.00|34:2.00|1:1.00\t2.0\t-\t199668378\t70.0\n')
#def test_fixed_wig(self):
#self.pk_cluster.write_as(FIXED_WIG)
#print self.pk_cluster.write_line()
def test_get_max_height_pos_bug2(self):
cluster = Cluster()
cluster.read_line("chr1 120967734 120967735 1:0.50|1:0.25")
self.assertEqual(cluster.write_line(), 'chr1\t120967734\t120967735\t1:0.50|1:0.25\t0.5\t.\t120967734\t0.75\n')
def test_variable_wig(self):
double_cluster = Cluster(read=PK, write=VARIABLE_WIG, rounding=True)
double_cluster.read_line('chr1 1 111 5:1|11:2|5:1|10:3|5:5|14:8|10:0.7|5:1|5:4|10:0.8|5:0.7|10:2|5:3|5:8|10:6|6:2')
"""print
print double_cluster.write_line()
double_cluster.write_as(WIG)"""
##################### END CONVERSION TESTS ############################################
"""
Adding disordered is no longer a feature
def test_add_disordered(self):
cluster = Cluster(read=BED)
cluster.read_line('chr1 101 150')
cluster.read_line('chr1 50 200')
self.assertEqual(cluster.write_line(), 'chr1\t50\t200\t51:1.00|50:2.00|50:1.00\n')
"""
def test_normalized_counts(self):
total_number_reads = 1e7
region = Region("chr1", 1, 300)
region_bed12 = Region("chr1", 1, 300, exome_size = 200)
c = Cluster(read=BED)
for i in range(0, 5):
c.read_line("chr1 1 100")
region.add_tags(c, True)
region_bed12.add_tags(c, True)
c.clear()
self.assertEqual(region.normalized_counts(), 5.) #simple-counts
self.assertEqual(region.normalized_counts(region_norm=True, total_n_norm=True, total_reads = total_number_reads), 1.666666666666667) #rpkm
self.assertEqual(region_bed12.normalized_counts(region_norm=True, total_n_norm=True, total_reads = total_number_reads), 2.5) #rpkm with exon_size
self.assertEqual(region.normalized_counts(pseudocount=True), 6.) #with pseudocounts
self.assertEqual(region.normalized_counts(region_norm=True, total_n_norm=True, total_reads = total_number_reads, regions_analyzed=10000, pseudocount=True), 1.998001998001998)
def test_max_height_pos(self):
cluster = Cluster(rounding=True, read=PK, write=PK)
cluster.read_line('chr1 101 142 4:1|1:2|2:1|3:4|29:5|2:2|1:1')
self.assertEqual(cluster.max_height_pos(), 125)
def test_bug_contiguous_peaks(self):
cluster = Cluster(rounding=True, read=PK, write=PK)
cluster2 = Cluster(rounding=True, read=PK, write=PK)
cluster.read_line('chr1 849917 850408 8:2|10:4|80:5|23:6|29:7|8:5|10:3|39:2|12:3|29:4|5:3|18:4|41:3|30:4|15:5|12:4|34:3|59:2|30:1')
cluster2.read_line('chr1 850408 850648 66:2|25:3|59:4|66:2|25:1 +')
result = cluster + cluster2
self.assertTrue(cluster.intersects(cluster2))
def test_sub_and_print(self):
cluster = Cluster()
cluster2 = Cluster(write_half_open=False)
cluster.read_line('chr1 1 1000 10:2|10:4|80:5|500:7|100:7|100:5')
cluster2.read_line('chr1 11 1000 10:4|80:5|500:6|100:7|99:5|1:4.99')
cluster2 = cluster - cluster2
self.assertEqual(cluster2.write_line(), 'chr1\t1\t10\t10:2.00\t2.0\t.\t5\t20.0\nchr1\t101\t600\t500:1.00\t1.0\t.\t350\t500.0\nchr1\t800\t800\t1:0.01\t0.01\t.\t800\t0.01\n')
#cluster2.write_as(PK, True)
#self.assertEqual(cluster2.write_line(), 'chr1\t1\t10\t10:2.00\t2.0\t.\t5\t520.01\nchr1\t100\t600\t500:1.00\t1.0\t.\t5\t520.01\nchr1\t799\t800\t1:0.01\t0.01\t.\t5\t520.01\n')
def test_intersects(self):
self.assertTrue(Cluster('chr1', 1, 10).intersects(Cluster('chr1', 10, 14)))
self.assertFalse(Cluster('chr2', 1, 10).intersects(Cluster('chr1', 4, 14)))
self.assertTrue(Cluster('chr1', 1, 10).intersects(Cluster('chr1', 4, 14)))
cluster = Cluster(read=PK, rounding=True)
cluster.read_line('chr1 1 100 100:1')
cluster2 = Cluster(read=PK,rounding=True)
cluster2.read_line('chr1 100 199 100:1')
result = cluster + cluster2
self.assertTrue(cluster.intersects(cluster2))
def test_intersects2(self):
cluster = Cluster(read=PK, rounding=True)
cluster.read_line('chr1 1 100 100:1')
cluster2 = Cluster(read=PK,rounding=True)
cluster2.read_line('chr1 5 50 100:1')
self.assertTrue(cluster.intersects(cluster2))
def test_subtract_with_gaps(self):
cluster1 = Cluster()
cluster2 = Cluster()
cluster1.read_line("chr2 1 100 30:1|50:2|40:1|3000:3")
cluster2.read_line("chr2 1 100 30:1|50:0|40:1|200:0|5000:1")
cluster1 -= cluster2
self.assertEqual(cluster1._profile, [[50, 2.0], [40, 0.0], [200, 3.0], [2800, 2.0]])
def test_subtract_with_gaps(self):
"""
238c238
< chr17 147132 147296 5:1.00|22:2.00|37:1.00|37:2.00|64:1.00 2.0 . 147180 224.0
---
> chr17 147132 147260 5:1.00|22:2.00|37:1.00|37:2.00|28:1.00 2.0 . 147180 188.0
experiment
chr17 146970 147070
chr17 147058 147158
chr17 147132 147232
chr17 147196 147296
chr17 147303 147403
chr17 147445 147545
chr17 147461 147561
control
chr17 146904 147004
chr17 147036 147136
chr17 147261 147361
chr17 147437 147537
chr17 147472 147572
chr17 147472 147572
"""
exp_cached = Cluster(cached=True)
control0 = Cluster(read=BED, cached=True)
control1 = Cluster(read=BED, cached=True)
control2 = Cluster(read=BED, cached=True)
control3 = Cluster(read=BED, cached=True)
control4 = Cluster(read=BED, cached=True)
#experiment.bed
exp_cached.read_line("chr17 146970 147296 88:1.00|13:2.00|61:1.00|27:2.00|37:1.00|37:2.00|64:1.00 2.0 . 147139 404.0")
#print exp_cached.write_line()
#control.bed
r = Region("chr17", 1, 2000)
control0.read_line("chr17 146904 147004")
control1.read_line("chr17 147036 147136")
control2.read_line("chr17 147261 147361")
control3.read_line("chr17 147437 147537")
control4.read_line("chr17 147472 147572")
r.add_tags([control1, control2])
meta = r.get_metacluster()
#print meta._profile
exp_cached -= meta
#print "CACHED:\n", exp_cached.write_line()
def test_bug_is_artifact(self):
cluster = Cluster(rounding=True)
cluster.read_line('chr1 10505760 10505928 8:4|3:5|5:6|8:8|2:10|1:11|5:12|3:15|2:16|2:16|3:18|7:20|3:19|57:20|21:19|8:15|3:14|5:13|8:11|2:9|1:8|5:7|3:4|2:3|2:3')
self.assertTrue(cluster.is_artifact(0.3))
def test_split(self):
double_cluster = Cluster(rounding=True)
double_cluster.read_line('chr1 100 215 5:1|10:5|5:7|5:80|5:1|5:40|15:1|10:2|5:3|5:8|10:6|10:5|10:4|10:3|6:2')
results = double_cluster.split(0.01)
correct_clusters = [Cluster(rounding=True), Cluster(rounding=True), Cluster(rounding=True)]
correct_clusters[0].read_line('chr1 100 125 5:1|10:5|5:7|5:80|2:1')
correct_clusters[1].read_line('chr1 128 141 2:1|5:40|7:1')
correct_clusters[2].read_line('chr1 143 215 7:1|10:2|5:3|5:8|10:6|10:5|10:4|10:3|6:2')
for i in range (0,len(correct_clusters)):
self.assertEqual(results[i].write_line(), correct_clusters[i].write_line())
def test_is_artifact(self):
artifact = Cluster(read=PK, write=PK, rounding=True)
artifact.read_line('chr1 1 111 5:1|100:4|6:2')
almost_not_artifact = Cluster(read=PK, write=PK, rounding=True)
almost_not_artifact.read_line('chr1 1 100 35:1|30:4|35:1')
almost_artifact = Cluster(read=PK, write=PK, rounding=True)
almost_artifact.read_line('chr1 1 99 45:1|25:4|30:1')
almost_artifact._recalculate_end()
self.assertTrue(artifact.is_artifact())
self.assertFalse(almost_not_artifact.is_artifact()) #with the changes for version 0.6.1, this line IS an artifact
self.assertFalse(almost_artifact.is_artifact())
def test_is_significant(self):
cluster = Cluster(rounding=True)
cluster.read_line('chr1 1 15 4:1|1:2|2:1|3:4|2:5|2:2|1:1') #area 35
self.assertTrue(cluster.is_significant(5, "numreads"))
self.assertTrue(cluster.is_significant(34, "numreads"))
self.assertFalse(cluster.is_significant(36, "numreads"))
self.assertFalse(cluster.is_significant(20))
self.assertTrue(cluster.is_significant(1))
self.assertTrue(cluster.is_significant(5))
def test_tag_eq_override(self):
tag1 = Cluster('M', 1, 100)
tag2 = Cluster('M', 1, 100)
tag3 = Cluster('X', 2, 140)
self.assertEqual(tag1, tag2)
self.assertNotEqual(tag1, tag3)
def test_nonzero(self):
tag = Cluster()
self.assertTrue(not tag)
tag.read_line("chr1 1 100 100:1")
self.assertFalse(not tag)
def test_comparison(self):
cluster = Region("chr1", 1, 100)
clusterdup = Cluster(read=BED)
clusterdup.read_line("chr1 1 100")
cluster2 = Cluster(read=BED)
cluster2.read_line("chr4 1000 1010")
cluster3 = Cluster(read=BED)
cluster3.read_line("chr5 3 103")
self.assertTrue(cluster < cluster2)
self.assertTrue(cluster2 < cluster3)
self.assertFalse(cluster > cluster3)
self.assertFalse(cluster < clusterdup)
self.assertTrue(cluster <= clusterdup)
def test_eq(self):
cluster = Cluster(read=PK)
cluster2 = Cluster(read=PK)
cluster3 = Cluster(read=PK)
cluster.read_line('chr1 1 15 4:1|1:2|2:1|3:4|2:5|2:2|1:1')
cluster2.read_line('chr1 1 15 4:1|1:2|2:1|3:4|2:5|2:2|1:1')
cluster3.read_line('chr1 1 15 4:1|1:2|2:1|3:4|2:5|2:2')
self.assertEqual(cluster, cluster2)
self.assertNotEqual(cluster, cluster3)
def test_extend(self):
cluster = Cluster(read=BED)
cluster.read_line('chr3 1 35 noname 666 +')
cluster2 = Cluster(read=BED)
cluster2.read_line('chr3 56 100 noname 666 -')
cluster.extend(100)
cluster2.extend(100)
self.assertEqual(cluster.write_line(), 'chr3\t1\t100\t100:1.00\t1.0\t+\t50\t100.0\n')
self.assertEqual(cluster2.write_line(), 'chr3\t1\t100\t100:1.00\t1.0\t-\t50\t100.0\n')
def test_extend_bug(self):
cluster = Cluster(read=BED, write=PK)
cluster.read_line('chr3 1 35 666 noname +')
cluster2 = Cluster(read=BED, write=PK)
cluster2.read_line('chr3 156 200 666 noname -')
cluster.extend(100)
cluster2.extend(100)
result = cluster + cluster2
self.assertEqual(200, len(result))
def test_extreme_split(self):
cluster = Cluster()
cluster.read_line('chr3 1 35 20:5|20:0|30:4')
clusters = cluster.absolute_split(threshold=0)
self.assertEqual(len(clusters), 2)
def test_is_singleton(self):
self.assertFalse(self.cluster_short.is_singleton())
self.assertTrue(self.bed_tag.is_singleton())
cluster = Cluster(read=PK)
cluster.read_line("chr1 1 100 100:2")
self.assertFalse(cluster.is_singleton())
def test_cluster_to_tag(self):
self.cluster_short.set_tag_length(10)
tags = self.cluster_short.decompose()
for tag in range(0, len(self.tag_list_short)):
self.assertEqual(self.tag_list_short[tag], tags[tag])
def test_decompose_alobestia(self):
super_cluster = Cluster(read=PK, write= BED, tag_length=130)
super_cluster.read_line("chrX 2895999 2896606 10:1|42:2|14:6|33:7|31:10|6:9|4:10|25:9|2:10|1:12|3:13|5:14|6:15|5:12|4:13|5:14|4:13|8:15|13:16|6:18|2:19|5:16|15:17|17:18|29:17|2:16|1:14|2:13|1:16|5:15|6:14|5:13|4:12|5:11|4:12|8:10|10:9|3:11|6:9|7:8|8:7|7:10|2:9|37:10|12:12|26:9|2:8|2:10|18:12|24:12|9:9|37:8|40:6|2:4|18:2")
tags = super_cluster.decompose()
for tag in tags:
self.assertEqual(len(tag), 130)
def test_is_contiguous_wig(self):
cluster = Cluster(read=WIG, read_half_open=True)
cluster.read_line('chr1 1599888 1599949 1.77')
cluster2 = Cluster(read=WIG, write=WIG, read_half_open=True)
cluster2.read_line('chr1 1599949 1600001 2.65')
#print cluster2.write_line()
self.assertTrue(cluster.is_contiguous(cluster2))
def test_is_contiguous_pk(self):
cluster = Cluster(read=PK, rounding=True)
cluster.read_line('chr1 1 100 100:1')
cluster2 = Cluster(read=PK,rounding=True)
cluster2.read_line('chr1 101 200 100:1')
self.assertTrue(cluster.is_contiguous(cluster2))
def test_write_pseudoeland(self):
self.bed_tag.write_as(ELAND)
self.bed_tag.write_line()
def test_write_pk(self):
cluster = Cluster(write=PK, name='chr5', start=1, rounding=True, write_half_open=True)
cluster.append_level(100, 1)
cluster.append_level(50, 2)
cluster.append_level(50, 3)
cluster.append_level(100, 1)
cluster.append_level(200, 0)
cluster.append_level(1, 3)
cluster.append_level(10, 0)
cluster.append_level(100, 1)
self.assertEqual(cluster.write_line(), 'chr5\t0\t300\t100:1|50:2|50:3|100:1\t3.0\t.\t175\t450.0\nchr5\t500\t501\t1:3\t3.0\t.\t501\t3.0\nchr5\t511\t611\t100:1\t1.0\t.\t561\t100.0\n') #HALF OPEN
cluster.write_as(PK, False) #Now write it as closed
self.assertEqual(cluster.write_line(),'chr5\t1\t300\t100:1|50:2|50:3|100:1\t3.0\t.\t175\t450.0\nchr5\t501\t501\t1:3\t3.0\t.\t501\t3.0\nchr5\t512\t611\t100:1\t1.0\t.\t561\t100.0\n') #Closed
def test_read_wig(self):
cluster1 = Cluster(read=WIG, name='chr5', start=1, rounding=True, read_half_open=True)
cluster1.read_line('chr6 0 100 1')
cluster2 = Cluster(read=WIG, name='chr5', start=1, rounding=True, read_half_open=False)
cluster2.read_line('chr6 1 100 1')
self.assertEqual(cluster1, cluster2)
def test_pk_print_empty(self):
cluster1 = Cluster(write=PK)
self.assertEqual(cluster1.write_line(), '')
cluster1.write_as(WIG)
self.assertEqual(cluster1.write_line(), '')
cluster1.write_as(BED)
self.assertEqual(cluster1.write_line(), '')
cluster1.write_as(ELAND)
self.assertEqual(cluster1.write_line(), '')
def test_is_singleton_error(self):
cluster = Cluster(read=PK, write=PK)
self.assertEqual(cluster.is_singleton(), False)
def test_is_empty(self):
cluster = Cluster(read=BED)
self.assertEqual(cluster.is_empty(), True)
cluster.read_line('chr1 10 130 666 hola +')
self.assertEqual(cluster.is_empty(), False)
cluster = Cluster(read=PK)
self.assertEqual(cluster.is_empty(), True)
cluster.read_line('chr1 1 15 4:1|1:2|2:1|3:4|2:5|2:2|1:1')
self.assertEqual(cluster.is_empty(), False)
cluster2 = Cluster(read=PK)
cluster2.read_line('chr1 1 15 4:1|1:2|2:1|3:4|2:5|2:2|1:1')
result = cluster - cluster2
self.assertEqual(result.is_empty(), True)
def test_max_height(self):
cluster = Cluster(read=PK)
cluster.read_line('chr1 1 15 4:1|1:2|2:10|3:4|2:15|2:2|1:1')
self.assertEqual(cluster.max_height(), 15)
def test_add_bed(self):
cluster1 = Cluster(read=BED)
cluster2 = Cluster(read=BED)
cluster3 = Cluster(read=BED)
cluster4 = Cluster(read=BED)
cluster5 = Cluster(read=BED)
cluster6 = Cluster(read=BED)
cluster1.read_line('chr1 1 100 666 hola +')
cluster2.read_line('chr1 1 100 666 hola +')
cluster3.read_line('chr1 1 50 666 hola +')
cluster4.read_line('chr1 10 145 666 hola +')
cluster5.read_line('chr1 45 95 666 hola +')
cluster6.read_line('chr1 1 200 666 hola +')
result1 = cluster1 + cluster2
result2 = cluster1 + cluster3
result3 = cluster4 + cluster1
#result4 = cluster1 + cluster3 + cluster4
result5 = cluster1 + cluster5
result6 = cluster1 + cluster6
self.assertEqual(result1.write_line(), 'chr1\t1\t100\t100:2.00\t2.0\t+\t50\t200.0\n')
self.assertEqual(result2.write_line(), 'chr1\t1\t100\t50:2.00|50:1.00\t2.0\t+\t25\t150.0\n')
self.assertEqual(result3.write_line(), 'chr1\t1\t145\t9:1.00|91:2.00|45:1.00\t2.0\t+\t55\t236.0\n')
#self.assertEqual(result4.write_line(), 'chr1\t1\t145\t9:2.00|41:3.00|50:2.00|45:1.00\n')
self.assertEqual(result5.write_line(), 'chr1\t1\t100\t44:1.00|51:2.00|5:1.00\t2.0\t+\t70\t151.0\n')
#self.assertEqual(result6.write_line(), 'chr1\t1\t200\t100:2.00|100:1.00\n')
def test_add2(self):
cluster = Cluster(read=BED)
cluster.read_line('chr1 1 20000 666 hola +')
cluster.read_line('chr1 1 20000 666 hola +')
cluster.read_line('chr1 1 20000 666 hola +')
cluster.read_line('chr1 1001 20000 666 hola +')
self.assertEqual(cluster.write_line(), 'chr1\t1\t20000\t1000:3.00|19000:4.00\t4.0\t+\t10500\t79000.0\n')
def test_add_pk(self):
cluster1 = Cluster(read=PK)
cluster2 = Cluster(read=PK)
cluster1.read_line('chr1\t1\t145\t9:2.00|41:3.00|50:2.00|45:1.00\n')
cluster2.read_line('chr1\t1\t125\t9:4.00|41:3.00|30:2.00|45:1.00\n')
result = cluster1 + cluster2
self.assertEqual(result.write_line(), 'chr1\t1\t145\t50:6.00|30:4.00|20:3.00|25:2.00|20:1.00\t6.0\t.\t25\t550.0\n')
def test_cluster_pk(self):
cluster = Cluster(read=PK)
cluster.read_line('chr1\t1\t145\t9:2.00|41:3.00|50:2.00|45:1.00\n')
cluster.read_line('chr1\t1\t125\t9:4.00|41:3.00|30:2.00|45:1.00\n')
self.assertEqual(cluster.write_line(), 'chr1\t1\t145\t50:6.00|30:4.00|20:3.00|25:2.00|20:1.00\t6.0\t.\t25\t550.0\n')
#def test_add_differentchr(self):
# self.assertRaises(DifferentChromosome, self.DifferentChromosome)
def read_invalid_lines(self):
cluster = Cluster(read=SAM)
for i in range(100):
cluster.read_line('chr1 1 15 4:1|1:2|2:10|3:4|2:15|2:2|1:1')
def test_read_invalid_lines(self):
self.assertRaises(InvalidLine, self.read_invalid_lines)
def DifferentChromosome(self):
cluster1 = Cluster(read=PK)
cluster1.read_line('chr1 1 15 4:1|1:2|2:10|3:4|2:15|2:2|1:1')
cluster2 = Cluster(read=PK)
cluster2.read_line('chr2 1 15 4:1|1:2|2:10|3:4|2:15|2:2|1:1')
a = cluster1 +cluster2
